Are you running an Exchange 2010 Hybrid Deployment server?
It sounds like you may not have the correct domain names in the Organizational Relationship.
Does this look like your issue? http://support.microsoft.com/kb/2667844

This is what I get whenever I attempt to the Get-OrganizationRelationship commandlet on both the hybrid server and the Exchange 2007 server:

The term 'Get-OrganizationRelationship' is not recognized as the name of a cmdlet, function, script
file, or operable program. Check the spelling of the name, or if a path was included, verify that
the path is correct and try again.
At line:1 char:29
+ Get-OrganizationRelationship <<<< |fl FreeBusyAccessEnabled,FreeBusyAccessLevel
+ CategoryInfo : ObjectNotFound: (Get-OrganizationRelationship:String) [], CommandNot
FoundException
+ FullyQualifiedErrorId : CommandNotFoundException

The term 'Get-OrganizationRelationship' is not recognized as the name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify thatthe path is correct and try again.At line:1 char:29+ Get-OrganizationRelationship <<<< |fl FreeBusyAccessEnabled,FreeBusyAccessLevel + CategoryInfo : ObjectNotFound: (Get-OrganizationRelationship:String) [], CommandNot FoundException + FullyQualifiedErrorId : CommandNotFoundException

Highfive is so simple that setting up every meeting room takes just minutes and every employee will be able to start or join a call from any room with ease. Never be called into a meeting just to get it started again. This is how video conferencing should work!

I ran the Get-OrganizationRelationship |fl FreeBusyAccessEnabled,FreeBusyAccessLevel commandlet in a regular powershell instance not a EMS instance. Below is the output I received when I ran the commandlet in EMS on my Exchange 2013 hybrid:

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